Replication Data for: Selection on ancestral genetic variation fuels repeated ecotype formation in bottlenose dolphins

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Louis, M.; Galimberti, M.; Archer, F.; Berrow, S.; Brownlow, A.; Fallon, R.; Nykänen, M.; O’brien, J.; Roberston, K. M.; Rosel, P. E.; Simon-Bouhet, B.; Wegmann, D.; Fontaine, M. C.; Foote, A. D.; Gaggiotti, O. E., 2021, "Replication Data for: Selection on ancestral genetic variation fuels repeated ecotype formation in bottlenose dolphins", https://doi.org/10.23708/Q2MYHE, DataSuds, V2

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Description	Data from Louis M., Galimberti M, Archer F., Berrow S., Brownlow A., Fallon R., O'Brien J., Robertson K., Rosel P. E., Simon-Bouhet B., Wegmann D., Fontaine M. C. , Foote A. D., Gaggiotti O. E.. 2021. Selection on ancestral genetic variation fuels repeated ecotype formation in bottlenose dolphins. (these authors contributed equally). See materials and methods and supplementary material for details on data generation. This data archive includes 4 main files : The VCF file (called genotypes) 1_TtmappednewTtvar_biallelic.vcf.gz: Variant calling format (VCF) file including the biallelic single nucleotide variants (SNVs or SNPs) used in Louis et al. The sample names are in the vcf file header. See the materials and methods and supplementary material of the manuscript for details on data generation. Genotype likelihood Linkage-disequilibrium pruned input file 2_Tursiops_unlinkedSNPs.beagle.gz: Note that the sample order (Ind0 to Ind55) is given in the file Tursiops_samples_no7Tt182.bamlist. Sample 7Tt182 is not included in the beagle file due to its low coverage but clusters with the other NWAp. See materials and methods and supplementary material for details on data generation. haplo file (pseudo-haploid random call) 3_Tursiops_ALL.haplo: Individual order is given in Tursiops_samples_ALL.bamlist. Note that 7Tt182 is included there but was not included in the analyses, which are based on a subset of individuals (one coastal individual and all allopatric pelagic individuals except from 7Tt192).See materials and methods and supplementary material for details on data generation. GhostAncestry-master compressed folder (4_GhostAncestry-master.tar.gz) contains the codes written by Benoit Simon-Bouhet to generate the input files for the ghost ancestry analyses - also available at https://github.com/besibo/GhostAncestry ## The folder 1_One Scaffold contains the code to test the script on one scaffold only ## The folder 2_All scaffolds contains the code to run the script on all scaffolds # R code is FileMaker.R, note that you will need the script Custom_functions.R as well # Example input files are in _infiles # Example output files are in _outfiles - the input files for the ghost ancestry analyses from Skov et al. 2018. See materials and methods and supplementary material for details on data generation.
Subject	Medicine, Health and Life Sciences
Related Publication	Louis, M., Galimberti, M., Archer, F., Berrow, S., Brownlow, A., Fallon, R., Nykänen, M., O'Brien, J., Robertson, K. M., Rosel, P. E., Simon-Bouhet, B., Wegmann, D., Fontaine, M. C., Foote, A. D., Gaggiotti, O. E. (2021) Selection on ancestral genetic variation fuels repeated ecotype formation in bottlenose dolphins. Science Advances, 7(44). doi: 10.1126/sciadv.abg1245
Notes	Data Type: Observational data; Other data
License/Data Use Agreement	Custom Dataset Terms

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	1_TtmappednewTtvar_biallelic.vcf.gz Ancestral_genetic_variants_bottlenose_dolphins/Gzip Archive - 704.4 MB Published Sep 2, 2021 12 Downloads MD5: 4461877afe51bc505f570808593aa7c0 Variant calling format (VCF) file including the biallelic single nucleotide variants (SNVs or SNPs) used in Louis et al. The sample names are in the vcf file header. See the materials and methods and supplementary material of the manuscript for details on data generation. Data	Access File File Access Public Download Options Gzip Archive Download Metadata Data File Citation EndNote XML RIS BibTeX
	2_Tursiops_unlinkedSNPs.beagle.gz Ancestral_genetic_variants_bottlenose_dolphins/Gzip Archive - 85.1 MB Published Sep 2, 2021 7 Downloads MD5: 8fe3f103955bdd7dd145c316dc008fe6 Genotype likelihood LD pruned input file in Beagle format. Note that Sample order (Ind0 to Ind55) is given in the file Tursiops_samples_no7Tt182.bamlist. Sample 7Tt182 is not included in the beagle file due to its low coverage but clusters with the other NWAp. See materials and methods and supplementary material for details on data generation. Data	Access File File Access Public Download Options Gzip Archive Download Metadata Data File Citation EndNote XML RIS BibTeX
	3_Tursiops_ALL.haplo.gz Ancestral_genetic_variants_bottlenose_dolphins/Gzip Archive - 108.0 MB Published Sep 2, 2021 5 Downloads MD5: e7909efb3649e2ac35f3cb17268be917 haplo file (pseudo-haploid random call): samples order is given in Tursiops_samples_ALL.bamlist. Note that 7Tt182 is included, but was not included in the analyses, which are based on subset of individuals (one coastal individual and all allopatric pelagic individuals except from 7Tt192). See materials and methods and supplementary material for details on data generation. Data	Access File File Access Public Download Options Gzip Archive Download Metadata Data File Citation EndNote XML RIS BibTeX
	4_GhostAncestry-master.tar.gz Ancestral_genetic_variants_bottlenose_dolphins/Gzip Archive - 8.8 KB Published Sep 2, 2021 4 Downloads MD5: d5234dbb967ad08679ed0eb346e3308e GhostAncestry-master contains the codes written by Benoit Simon-Bouhet to generate the input files for the ghost ancestry analyses - also available at https://github.com/besibo/GhostAncestry ## The folder 1_One Scaffold contains the code to test the script on one scaffold only ## The folder 2_All scaffolds contains the code to run the script on all scaffolds # R code is FileMaker.R, note that you will need the script Custom_functions.R as well # Example input files are in _infiles # Example output files are in _outfiles - the input files for the ghost ancestry analyses from Skov et al. 2018. See materials and methods and supplementary material for details on data generation. Code	Access File File Access Public Download Options Gzip Archive Download Metadata Data File Citation EndNote XML RIS BibTeX
	Tursiop_samples_ALL.bamlist.txt Ancestral_genetic_variants_bottlenose_dolphins/Unknown - 351 B Published Sep 2, 2021 6 Downloads MD5: 8b7e2ce3192a5f460626c00d41c18f65 Names of the samples and their order. See materials and methods and supplementary material for details on data generation Data	Access File File Access Public Download Options Original File Format Download Metadata Data File Citation EndNote XML RIS BibTeX
	Tursiop_samples_no7Tt182.bamlist.txt Ancestral_genetic_variants_bottlenose_dolphins/Unknown - 344 B Published Sep 2, 2021 7 Downloads MD5: 734cebd2c7212d5a5b48cead8ebd0d42 Names of the samples and their order, after excluding sample 7Tt182. See materials and methods and supplementary material for details on data generation Data	Access File File Access Public Download Options Original File Format Download Metadata Data File Citation EndNote XML RIS BibTeX

Citation Metadata

Persistent Identifier	doi:10.23708/Q2MYHE
Publication Date	2021-09-02
Title	Replication Data for: Selection on ancestral genetic variation fuels repeated ecotype formation in bottlenose dolphins
Subtitle	The genomics of ecotype formation in dolphins
Author	Louis, M. (Scottish Oceans Institute, University of St Andrews, East Sands, St Andrews KY16 8LB, Scotland, UK) Galimberti, M. (Department of Biology and Biochemistry, University of Fribourg, Fribourg, Switzerland) Archer, F. (National Marine Fisheries Service, Southwest Fisheries Science Center, NOAA, 8901 La Jolla Shores Drive, La Jolla, CA 92037, USA) Berrow, S. (Irish Whale and Dolphin Group, Kilrush, Co Clare, Ireland) Brownlow, A. (Scottish Marine Animal Stranding Scheme, SRUC Northern Faculty, An Lòchran, Inverness Campus, IV2 5NA,UK) Fallon, R. (School of Medicine, University of St Andrews, North HaughSt Andrews, Fife, KY16 9TF, Scotland, UK) Nykänen, M. (University College Cork, Cork, Ireland) O’brien, J. (Irish Whale and Dolphin Group, Kilrush, Co Clare, Ireland) Roberston, K. M. (National Marine Fisheries Service, Southwest Fisheries Science Center, NOAA, 8901 La Jolla Shores Drive, La Jolla, CA 92037, USA) Rosel, P. E. (National Marine Fisheries Service, Southeast Fisheries Science Center, NOAA, 646 Cajundome Boulevard, Lafayette, LA 70506, USA) Simon-Bouhet, B. (Centre d’Etudes Biologiques de Chize, Universite de La Rochelle 17000 La Rochelle, France) Wegmann, D. (Department of Biology and Biochemistry, University of Fribourg, Fribourg, Switzerland) Fontaine, M. C. (UMR MIVEGEC - CNRS, IRD, Univ. Montpellier - France) Foote, A. D. (Molecular Ecology Fisheries Genetics Lab, School of Biological Sciences, Bangor University, Bangor, UK) Gaggiotti, O. E. (Scottish Oceans Institute, University of St Andrews, East Sands, St Andrews KY16 8LB, Scotland, UK)
Point of Contact	Use email button above to contact. Louis, Marie (Scottish Oceans Institute, U. St Andrews, Scotland, UK) Fontaine, Michael C. (UMR MIVEGEC - CNRS, IRD, Univ. Montpellier - France) Foote, Andrew D. (Department of Natural History, NTNU, Trondheim, Norway) Gaggiotti, Oscar (Scottish Oceans Institute, U. St Andrews, Scotland, UK)
Description	Data from Louis M., Galimberti M, Archer F., Berrow S., Brownlow A., Fallon R., O'Brien J., Robertson K., Rosel P. E., Simon-Bouhet B., Wegmann D., Fontaine M. C. , Foote A. D., Gaggiotti O. E.. 2021. Selection on ancestral genetic variation fuels repeated ecotype formation in bottlenose dolphins. (these authors contributed equally). See materials and methods and supplementary material for details on data generation. This data archive includes 4 main files : The VCF file (called genotypes) 1_TtmappednewTtvar_biallelic.vcf.gz: Variant calling format (VCF) file including the biallelic single nucleotide variants (SNVs or SNPs) used in Louis et al. The sample names are in the vcf file header. See the materials and methods and supplementary material of the manuscript for details on data generation. Genotype likelihood Linkage-disequilibrium pruned input file 2_Tursiops_unlinkedSNPs.beagle.gz: Note that the sample order (Ind0 to Ind55) is given in the file Tursiops_samples_no7Tt182.bamlist. Sample 7Tt182 is not included in the beagle file due to its low coverage but clusters with the other NWAp. See materials and methods and supplementary material for details on data generation. haplo file (pseudo-haploid random call) 3_Tursiops_ALL.haplo: Individual order is given in Tursiops_samples_ALL.bamlist. Note that 7Tt182 is included there but was not included in the analyses, which are based on a subset of individuals (one coastal individual and all allopatric pelagic individuals except from 7Tt192).See materials and methods and supplementary material for details on data generation. GhostAncestry-master compressed folder (4_GhostAncestry-master.tar.gz) contains the codes written by Benoit Simon-Bouhet to generate the input files for the ghost ancestry analyses - also available at https://github.com/besibo/GhostAncestry ## The folder 1_One Scaffold contains the code to test the script on one scaffold only ## The folder 2_All scaffolds contains the code to run the script on all scaffolds # R code is FileMaker.R, note that you will need the script Custom_functions.R as well # Example input files are in _infiles # Example output files are in _outfiles - the input files for the ghost ancestry analyses from Skov et al. 2018. See materials and methods and supplementary material for details on data generation.
Subject	Medicine, Health and Life Sciences
Scientific Theme	Continental waters and oceans: biology (NumeriSud) https://uri.ird.fr/so/kos/tnu/034 Aquatic ecosystems (NumeriSud) https://uri.ird.fr/so/kos/tnu/036 Zoology (NumeriSud) https://uri.ird.fr/so/kos/tnu/080
Related Publication	Louis, M., Galimberti, M., Archer, F., Berrow, S., Brownlow, A., Fallon, R., Nykänen, M., O'Brien, J., Robertson, K. M., Rosel, P. E., Simon-Bouhet, B., Wegmann, D., Fontaine, M. C., Foote, A. D., Gaggiotti, O. E. (2021) Selection on ancestral genetic variation fuels repeated ecotype formation in bottlenose dolphins. Science Advances, 7(44). doi: 10.1126/sciadv.abg1245 https://doi.org/10.1126/sciadv.abg1245
Notes	Data Type: Observational data; Other data
Language	English
Production Location	University of Groningen, Netherlands and University of St Andrews, UK
Funding Information	Total Foundation: Fellowship awarded to ML University of Groningen: Start up awarded to MCF Marine Alliance for Science and Technology for Scotland and The Russell Trust awarded to OEG Fyssen: Awarded to ML Godfrey Hewitt mobility award from the European Society for Evolutionary Biology (ESEB): Awarded to ML People’s Trust for Endangered Species Lerner-Gray Grants for Marine Research from the American Museum of Natural History the University of St Andrew European Union’s Horizon 2020: awarded to ADF Marie Skłodowska-Curie grant: No. 663830
Depositor	Fontaine, M. C.
Deposit Date	2021-09-01

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